Progress in the R ecosystem for representing and handling spatial data

Bivand, Roger

doi:10.1007/s10109-020-00336-0

Cited by 38 publications

(30 citation statements)

References 37 publications

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“…We made the engine openly available to the research community in an R package to catalyze an interdisciplinary exploration, application, and quantification of the mechanisms behind biodiversity dynamics. The R statistical programming language and environment [ 67 ] is widely used for reproducible and open-source research [ 68 , 69 ], and since its origins, it has been used for handling and analyzing spatial data [ 70 ]. Gen3sis follows best practices for scientific computing [ 71 ], including high modularization; consistent naming, style, and formatting; single and meaningful authoritative representation; automated workflows; version control; continuous integration; and extensive documentation.…”

Section: Introductionmentioning

confidence: 99%

gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity

et al. 2021

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Understanding the origins of biodiversity has been an aspiration since the days of early naturalists. The immense complexity of ecological, evolutionary, and spatial processes, however, has made this goal elusive to this day. Computer models serve progress in many scientific fields, but in the fields of macroecology and macroevolution, eco-evolutionary models are comparatively less developed. We present a general, spatially explicit, eco-evolutionary engine with a modular implementation that enables the modeling of multiple macroecological and macroevolutionary processes and feedbacks across representative spatiotemporally dynamic landscapes. Modeled processes can include species’ abiotic tolerances, biotic interactions, dispersal, speciation, and evolution of ecological traits. Commonly observed biodiversity patterns, such as α, β, and γ diversity, species ranges, ecological traits, and phylogenies, emerge as simulations proceed. As an illustration, we examine alternative hypotheses expected to have shaped the latitudinal diversity gradient (LDG) during the Earth’s Cenozoic era. Our exploratory simulations simultaneously produce multiple realistic biodiversity patterns, such as the LDG, current species richness, and range size frequencies, as well as phylogenetic metrics. The model engine is open source and available as an R package, enabling future exploration of various landscapes and biological processes, while outputs can be linked with a variety of empirical biodiversity patterns. This work represents a key toward a numeric, interdisciplinary, and mechanistic understanding of the physical and biological processes that shape Earth’s biodiversity.

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Section: Introductionmentioning

confidence: 99%

gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity

et al. 2021

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“…Yet many traditional transport planning tools focus on motor traffic, emphasising travel time savings impacts over environmental and health savings (Hall et al 1980;de Dios Ort'uzar and Willumsen 2011), often at low levels of geographic resolution (Hollander 2016). These observations have led to criticism of transport models which are deemed unable to represent transport network details such as pavement and way widths that are needed effectively designed for active transport (Parkin 2018) or capture community input (Beimborn and Kennedy 1996).…”

Section: Political Driversmentioning

confidence: 99%

Open source tools for geographic analysis in transport planning

Lovelace

2021

J Geogr Syst

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Geographic analysis has long supported transport plans that are appropriate to local contexts. Many incumbent ‘tools of the trade’ are proprietary and were developed to support growth in motor traffic, limiting their utility for transport planners who have been tasked with twenty-first century objectives such as enabling citizen participation, reducing pollution, and increasing levels of physical activity by getting more people walking and cycling. Geographic techniques—such as route analysis, network editing, localised impact assessment and interactive map visualisation—have great potential to support modern transport planning priorities. The aim of this paper is to explore emerging open source tools for geographic analysis in transport planning, with reference to the literature and a review of open source tools that are already being used. A key finding is that a growing number of options exist, challenging the current landscape of proprietary tools. These can be classified as command-line interface, graphical user interface or web-based user interface tools and by the framework in which they were implemented, with numerous tools released as R, Python and JavaScript packages, and QGIS plugins. The review found a diverse and rapidly evolving ‘ecosystem’ tools, with 25 tools that were designed for geographic analysis to support transport planning outlined in terms of their popularity and functionality based on online documentation. They ranged in size from single-purpose tools such as the QGIS plugin AwaP to sophisticated stand-alone multi-modal traffic simulation software such as MATSim, SUMO and Veins. Building on their ability to re-use the most effective components from other open source projects, developers of open source transport planning tools can avoid ‘reinventing the wheel’ and focus on innovation, the ‘gamified’ A/B Street https://github.com/dabreegster/abstreet/#abstreet simulation software, based on OpenStreetMap, a case in point. The paper, the source code of which can be found at https://github.com/robinlovelace/open-gat, concludes that, although many of the tools reviewed are still evolving and further research is needed to understand their relative strengths and barriers to uptake, open source tools for geographic analysis in transport planning already hold great potential to help generate the strategic visions of change and evidence that is needed by transport planners in the twenty-first century.

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“…2020-017 61 GIScience Code for spatial data handling, analysis, and visualisation using a variety of R packages 62 was checked after peer review before publication.…”

Section: -012 51 Covid-19mentioning

confidence: 99%

CODECHECK: an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility

Nüst

Eglen

2021

F1000Res

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The traditional scientific paper falls short of effectively communicating computational research. To help improve this situation, we propose a system by which the computational workflows underlying research articles are checked. The CODECHECK system uses open infrastructure and tools and can be integrated into review and publication processes in multiple ways. We describe these integrations along multiple dimensions (importance, who, openness, when). In collaboration with academic publishers and conferences, we demonstrate CODECHECK with 25 reproductions of diverse scientific publications. These CODECHECKs show that asking for reproducible workflows during a collaborative review can effectively improve executability. While CODECHECK has clear limitations, it may represent a building block in Open Science and publishing ecosystems for improving the reproducibility, appreciation, and, potentially, the quality of non-textual research artefacts. The CODECHECK website can be accessed here: https://codecheck.org.uk/.

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Progress in the R ecosystem for representing and handling spatial data

Cited by 38 publications

References 37 publications

gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity

gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity

Open source tools for geographic analysis in transport planning

CODECHECK: an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility

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